11-63304838-C-T

Position:

• chr11-63304838-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001039752.4(SLC22A10):​c.1547C>T​(p.Pro516Leu) variant causes a missense change. The variant allele was found at a frequency of 0.548 in 1,613,444 control chromosomes in the GnomAD database, including 247,086 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.48 (18863 hom., cov: 32)
  • Exomes 𝑓: 0.55 (228223 hom.)
• Consequence: SLC22A10 NM_001039752.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.82

Genes affected

SLC22A10 (HGNC:18057): (solute carrier family 22 member 10) Predicted to enable transmembrane transporter activity. Predicted to be involved in organic anion transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SLC22A10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=1.385808E-4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A10	NM_001039752.4	c.1547C>T	p.Pro516Leu	missense_variant	9/10	ENST00000332793.11	NP_001034841.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A10	ENST00000332793.11	c.1547C>T	p.Pro516Leu	missense_variant	9/10	1	NM_001039752.4	ENSP00000327569.6

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73404 AN: 151904 Hom.: 18871 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.500

GnomAD3 exomes AF: 0.520 AC: 129602 AN: 249020 Hom.: 34633 AF XY: 0.523 AC XY: 70657 AN XY: 135088

Gnomad AFR exome AF: 0.297

Gnomad AMR exome AF: 0.509

Gnomad ASJ exome AF: 0.444

Gnomad EAS exome AF: 0.421

Gnomad SAS exome AF: 0.453

Gnomad FIN exome AF: 0.606

Gnomad NFE exome AF: 0.578

Gnomad OTH exome AF: 0.536

GnomAD4 exome AF: 0.555 AC: 810684 AN: 1461422 Hom.: 228223 Cov.: 59 AF XY: 0.553 AC XY: 401901 AN XY: 727024

Gnomad4 AFR exome AF: 0.283

Gnomad4 AMR exome AF: 0.505

Gnomad4 ASJ exome AF: 0.430

Gnomad4 EAS exome AF: 0.413

Gnomad4 SAS exome AF: 0.459

Gnomad4 FIN exome AF: 0.609

Gnomad4 NFE exome AF: 0.579

Gnomad4 OTH exome AF: 0.536

GnomAD4 genome AF: 0.483 AC: 73411 AN: 152022 Hom.: 18863 Cov.: 32 AF XY: 0.482 AC XY: 35848 AN XY: 74322

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.499

Alfa AF: 0.554 Hom.: 58926

Bravo AF: 0.471

TwinsUK AF: 0.574 AC: 2130

ALSPAC AF: 0.571 AC: 2201

ESP6500AA AF: 0.294 AC: 1127

ESP6500EA AF: 0.568 AC: 4689

ExAC AF: 0.519 AC: 62659

Asia WGS AF: 0.474 AC: 1649 AN: 3478

EpiCase AF: 0.569

EpiControl AF: 0.578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.47
BayesDel_addAF	Benign	-0.42	T
BayesDel_noAF	Benign	-0.23
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.36	T
Eigen	Uncertain	0.47
Eigen_PC	Benign	0.22
FATHMM_MKL	Uncertain	0.77	D
LIST_S2	Uncertain	0.93	D
MetaRNN	Benign	0.00014	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Pathogenic	3.8	H
PrimateAI	Uncertain	0.49	T
PROVEAN	Pathogenic	-8.8	D
REVEL	Uncertain	0.41
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0020	D
Polyphen		1.0	D
Vest4		0.27
MPC		0.12
ClinPred		0.072	T
GERP RS		2.7
Varity_R		0.94
gMVP		0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1201559; hg19: chr11-63072310; COSMIC: COSV60420735; COSMIC: COSV60420735;